def _build_bowtie2_nodes(config, parameters, input_filename, tags, options):
if paths.is_paired_end(input_filename):
input_filename_1 = input_filename_2 = input_filename
else:
input_filename_1, input_filename_2 = input_filename, ""
params = Bowtie2Node.customize(input_file_1 = input_filename_1.format(Pair = 1),
input_file_2 = input_filename_2.format(Pair = 2),
threads = config.bowtie2_max_threads,
**parameters)
params.commands["convert"].set_option('-q', options["Aligners"]["Bowtie2"]["MinQuality"])
if options["QualityOffset"] == 64:
params.commands["aln"].set_option("--phred64")
elif options["QualityOffset"] == 33:
params.commands["aln"].set_option("--phred33")
else:
params.commands["aln"].set_option("--solexa-quals")
_apply_aln_user_parameters(options["Aligners"]["Bowtie2"], params, ("aln",))
pg_tag = "bowtie2:CL:%s" % (_build_bowtie_cl_tag(options).replace("%", "%%"),)
params.commands["convert"].add_option("--update-pg-tag", pg_tag)
params.commands["aln"].set_option("--rg-id", tags["ID"])
for tag_name in ("SM", "LB", "PU", "PL", "PG"):
if tag_name == "PG":
tag_value = tags["PG"].lower()
elif tag_name == "PU":
tag_value = tags["PU_src"]
else:
tag_value = tags[tag_name]
params.commands["aln"].add_option("--rg", "%s:%s" % (tag_name, tag_value))
return params.build_node()
def _bowtie2_build_nodes(config, parameters, tags, options):
params = Bowtie2Node.customize(threads=config.bowtie2_max_threads,
**parameters)
apply_options(params.commands["aln"], _bowtie2_aln_parameters(options))
pg_tags = "bowtie2:CL:%s" % (_bowtie2_build_cl_tag(options), )
_set_rg_tags(params.commands["convert"], tags, pg_tags)
return params
def _bowtie2_build_nodes(config, parameters, tags, options):
params = Bowtie2Node.customize(threads = config.bowtie2_max_threads,
**parameters)
apply_options(params.commands["aln"], _bowtie2_aln_parameters(options))
pg_tags = "bowtie2:CL:%s" % (_bowtie2_build_cl_tag(options),)
_set_rg_tags(params.commands["convert"], tags, pg_tags)
return params
def _bowtie2_aln_pe(config, index):
node_params = {"input_file_1" : "tests/data/sim_reads/mate_1.fastq.gz",
"input_file_2" : "tests/data/sim_reads/mate_2.fastq.gz",
"prefix" : os.path.join(config.destination, "rCRS"),
"reference" : "tests/data/rCRS.fasta",
"dependencies" : (config.dependencies, index)}
standard = Bowtie2Node(output_file = os.path.join(config.destination, "aln_pe_standard", "output.bam"),
**node_params)
custom = Bowtie2Node.customize(output_file = os.path.join(config.destination, "aln_pe_custom", "output.bam"),
**node_params)
custom.commands["aln"].set_option("--very-sensitive")
return MetaNode(description = "Bowtie2 aln PE",
dependencies = [standard, custom.build_node()])
def _bowtie2_aln_pe(config, index):
node_params = {
"input_file_1": "tests/data/sim_reads/mate_1.fastq.gz",
"input_file_2": "tests/data/sim_reads/mate_2.fastq.gz",
"prefix": os.path.join(config.destination, "rCRS"),
"reference": "tests/data/rCRS.fasta",
"dependencies": (config.dependencies, index)
}
standard = Bowtie2Node(output_file=os.path.join(config.destination,
"aln_pe_standard",
"output.bam"),
**node_params)
custom = Bowtie2Node.customize(output_file=os.path.join(
config.destination, "aln_pe_custom", "output.bam"),
**node_params)
custom.commands["aln"].set_option("--very-sensitive")
return MetaNode(description="Bowtie2 aln PE",
dependencies=[standard, custom.build_node()])
def _build_bowtie2_nodes(config, parameters, input_filename, tags, options):
if paths.is_paired_end(input_filename):
input_filename_1 = input_filename_2 = input_filename
else:
input_filename_1, input_filename_2 = input_filename, ""
params = Bowtie2Node.customize(
input_file_1=input_filename_1.format(Pair=1),
input_file_2=input_filename_2.format(Pair=2),
threads=config.bowtie2_max_threads,
**parameters)
params.commands["convert"].set_option(
'-q', options["Aligners"]["Bowtie2"]["MinQuality"])
if options["QualityOffset"] == 64:
params.commands["aln"].set_option("--phred64")
elif options["QualityOffset"] == 33:
params.commands["aln"].set_option("--phred33")
else:
params.commands["aln"].set_option("--solexa-quals")
_apply_aln_user_parameters(options["Aligners"]["Bowtie2"], params,
("aln", ))
pg_tag = "bowtie2:CL:%s" % (_build_bowtie_cl_tag(options).replace(
"%", "%%"), )
params.commands["convert"].add_option("--update-pg-tag", pg_tag)
params.commands["aln"].set_option("--rg-id", tags["ID"])
for tag_name in ("SM", "LB", "PU", "PL", "PG"):
if tag_name == "PG":
tag_value = tags["PG"].lower()
elif tag_name == "PU":
tag_value = tags["PU_src"]
else:
tag_value = tags[tag_name]
params.commands["aln"].add_option("--rg",
"%s:%s" % (tag_name, tag_value))
return params.build_node()